bioRxiv/medRxiv TRiP Review Activity

253 Reviews — GigaScience — Bioinformatics

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Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.
Chang, J. J.-Y., Yang, X., Teng, H., Reames, B., Corbin, V., Coin, L. J. M.
10.1101/2024.10.25.620206 — Posted: 2024-10-25 — Discussion: 2025-09-30  GigaScience
SPEX: A modular end-to-end analytics tool for spatially resolved omics of tissues
Pechuan Jorge, X., Li, X., Risom, T., Zubkov, A., Tabatsky, E., Prilipko, A., Ye, X., Shi, Z., Nowicka, m., Peale, F., Hibar, D., Ziai, J., Jesudason, R., Orlova, D.
10.1101/2022.08.22.504841 — Posted: 2022-08-23 — Discussion: 2025-09-30  GigaScience
Nanopore- and AI-empowered metagenomic viability inference
Urel, H., Benassou, S., Reska, T., Marti, H., Rayo, E., Martin, E. J., Schloter, M., Ferguson, J. M., Kesselheim, S., Borel, N., Urban, L.
10.1101/2024.06.10.598221 — Posted: 2024-06-11 — Discussion: 2025-09-30  GigaScience
SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework
Hua, Y., Weng, L., Zhao, F., Rambow, F.
10.1101/2024.08.01.606144 — Posted: 2024-08-04 — Discussion: 2025-08-04  GigaScience
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome
Barbosa, M. C., da Silva, J. F. M., Alves, L. C., Finn, R. D., Paschoal, A. R.
10.1101/2024.07.18.604052 — Posted: 2024-07-19 — Discussion: 2025-07-08  GigaScience
Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database
Ikeda, S., Zou, Z., Bono, H., Moriya, Y., Kawashima, S., Katayama, T., Oki, S., Ohta, T.
10.1101/2025.02.17.638570 — Posted: 2025-02-22 — Discussion: 2025-07-08  GigaScience
Analysis-ready VCF at Biobank scale using Zarr
Czech, E. A., Millar, T. R., White, T. E., Jeffery, B., Miles, A., Tallman, S., Wojdyla, R., Zabad, S., Hammerbacher, J., Kelleher, J.
10.1101/2024.06.11.598241 — Posted: 2024-06-12 — Discussion: 2025-07-08  GigaScience
Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset
Wess, M., Andersen, M. K., Midtbust, E., Guillem, J. C. C., Viset, T., Storkersen, O., Krossa, S., Rye, M., Tessem, M.-B.
10.1101/2024.06.11.598306 — Posted: 2024-06-12 — Discussion: 2025-06-03  GigaScience
External validation of machine learning models - registered models and adaptive sample splitting
Gallitto, G., Englert, R., Kincses, B., Kotikalapudi, R., Li, J., Bingel, U., Spisak, T.
10.1101/2023.12.01.569626 — Posted: 2023-12-04 — Discussion: 2025-06-03  GigaScience
Defining the limits of plant chemical space: challenges and estimations
Hart, C. E., Gadiya, Y., Kind, T., Krettler, C. A., Gaetz, M., Misra, B. B., Healey, D., Allen, A., Colluru, V., Domingo-Fernandez, D.
10.1101/2025.01.08.631938 — Posted: 2025-01-13 — Discussion: 2025-05-06  GigaScience

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